Dichroism Spectra Research Articles

Unfolding Dynamics of a Photoswitchable Helical Peptide

We present an atomistic force field for the azo-moiety of the photoswitchable FK-11-X peptide. We use the parameters to study the unfolding of the peptide through molecular dynamics simulations. The unfolded ensemble contains many different structures, ranging from a partially unfolded peptide to a fully unfolded structure. The averaged computed far-ultraviolet circular dichroism (CD) spectrum of the set of structures, which was simulated using the newly developed force field, agrees well with experiment. The rate of the simulated unfolding process was estimated to have a time constant of 5.80 ± 0.03 ns from the time evolution of the CD spectrum of the peptide, computed from the backbone conformations sampled over 40 simulated trajectories. Our estimated time constant is faster than, but not inconsistent with, previous experimental estimates from time-resolved infrared and optical rotatory dispersion spectroscopy.

Identification of Functional Interactome of Gastric Cancer Cells with Helicobacter pylori Outer Membrane Protein HpaA by HPLC-MS/MS.

HpaA as an outer membrane protein of Helicobacter pylori (H. pylori) plays a significant role in the adhesion to the human stomach, but the functional relation between HpaA and gastric epithelial cells is still not clear. To screen the interaction between HpaA and cellular proteins in gastric epithelial cells, the HpaA protein from H. pylori 26695 fused with a tag (6× His) was expressed and purified successfully, the secondary structure was estimated by the Circular Dichroism (CD) spectrum, and the purified recombinant protein was used to perform the pull-down assays with gastric cancer cell lines (AGS and SGC-7901) lysates, respectively. The pull-down proteins were identified by high-performance liquid chromatography tandem mass spectrometry system (HPLC-MS/MS). A total of 9 and 13 proteins related were analyzed from AGS and SGC-7901 cell lysates, respectively. ANXA2 was considered as putative HpaA functional partner discovered from lysates of both cell lines with high score and coverage. It is hypothesized that HpaA may be involved in the biological process of regulation of transcription and nucleic acid metabolism during the adhesion of H. pylori to human gastric epithelial cells, and HpaA-binding proteins also be used as targets for the development of antiadhesion drugs against H. pylori.

On Interpretation of Spectra of Photochemically Induced Circular Dichroism of Semiconductor Nanocrystals

We propose an approach to the analysis and interpretation of spectra of photoinduced circular dichroism (PICD) of semiconductor nanocrystals, in particular, quantum dots, based on comparison of these spectra with the spectra of magnetic circular dichroism (MCD). We show that MCD and PICD spectra have similar features. The values of parameters similar to the well-known parameters A and B of the MCD spectra, which characterize the splitting and mixing of states, are determined from the PICD spectra.

Facile fabrication of nano-, helical structure PMMA polymer with chiral nematic liquid crystal and AAO double templates

ABSTRACT Nanostructured helical polymers possess the desirable properties of nano-, helical materials and hold great promise in many fields. Template method is one of the easiest ways to control the shape and size of nanostructure materials. However, the nano- and helical polymers obtained using double template methods have rarely been studied. Here, chiral nematic liquid crystal (CLC) material and nanostructure anodically oxidised aluminium (AAO) were employed as templates to fabricate a novel nano-, helical structure PMMA polymer. In the preparation process, methyl methacrylate monomer was polymerised in the CLC template. Then, the polymer molecular infiltrated into the nanopores of AAO template by self-assembly technology. The morphology and molecular structure of the nano-, helical polymer were demonstrated by scanning electron microscopy, atomic force microscopy, and Fourier transform-infrared spectroscopy. The circular dichroism (CD) spectrum results demonstrated that the nano-, helical polymer CD curve was similar to that of CLC. Helical conformation of the obtained polymer was identified efficiently. The strategy for preparing nano-, helical polymers was highly efficient and low cost since it took the advantages of CLC and AAO templates. Thus, numerous advanced materials would be accessible by this approach.

Hyperacmosins H-J, three new polycyclic polyprenylated acylphloroglucinol derivatives from Hypericum acmosepalum

Three new polycyclic polyprenylated acylphloroglucinol derivatives, hyperacmosins H-J (1–3), with four known compounds (4–7), were isolated from the air-dried aerial parts of Hypericum acmosepalum. Especially, compounds 1 and 2 were identified as methylated polycyclic polyprenylated acylphloroglucinol derivatives (mPPAPs). Their structures were established by NMR, HRESIMS and experimental electronic circular dichroism (ECD) spectra. The hepatoprotective activity of seven compounds were evaluated. Compounds 1 and 5 exhibited hepatoprotective activity against paracetamol-induced HepG2 cell damage.

Influence of different aligning surfaces on the morphology of dichroic squaraine films

Dichroic organic films have found a broad application in various optoelectronic devices. One efficient method for the production of thin dichroic films is the deposition of the film onto aligning polymer surface. Scientists propose different explanations concerning the mechanisms of the molecules aligning. Here, we report the aligning of squaraine (Sq) molecules on the different aligning polymer surfaces, independent from the morphology of the Sq deposits. Aligned polytetrafluoroethylene (PTFE) layers were produced by either unidirectional hot friction transfer or by PTFE decomposition in vacuum with the activation of the gas by accelerated electrons and the consequent unidirectional rubbing with a cloth. Sq films grown on the aligned PTFE surfaces and on the nanostructured polycarbonate (PC) surfaces were found to exhibit dichroic optical absorption spectra. Despite different shape and orientation of the Sq crystals on the PTFE and the PC surfaces, the absorption of polarized light was shown to exhibit one pattern. Variations in the morphology of Sq films on different surfaces were explained by the competitive participation of different growth mechanisms, which depended on the properties of the deposited compound, the aligning layer and the growth conditions. The PTFE aligning layers can be useful in organic electronics due to low-temperature processing.

Pressure dependence of vibrational optical activity of model biomolecules. A computational study.

Change of molecular properties with pressure is an attracting means to regulate molecular reactivity or biological activity. However, the effect is usually small and so far explored rather scarcely. To obtain a deeper insight and estimate the sensitivity of vibrational optical activity spectra to pressure-induced conformational changes, we investigate small model molecules. The Ala-Ala dipeptide, isomaltose disaccharide and adenine-uracil dinucleotide were chosen to represent three different biomolecular classes. The pressure effects were modeled by molecular dynamics and density functional theory simulations. The dinucleotide was found to be the most sensitive to the pressure, whereas for the disaccharide the smallest changes are predicted. Pressure-induced relative intensity changes in vibrational circular dichroism and Raman optical activity spectra are predicted to be 2-3-times larger than for non-polarized IR and Raman techniques.

In-Gel Probing Polymorphic Structures of G-Quadruplexes Derived from c-Myc Promoter

Abstract Some G-quadruplex (G4) forming sequences are able to form multimers under physiological conditions, which limits the structure-activity study of G4s. Here we report an in-gel visual method to probe the conformational polymorphism of the derivatives of a parallel G4-forming sequence, c-Myc by flanking with different A/T bases and typical intermolecular G4-forming sequences. Fluorescence and circular dichroism (CD) spectra showed that the interaction of c-Myc derivatives with Thioflavin T (ThT) caused different fluorescence enhancements of ThT, and intermolecular parallel G4s caused higher fluorescence enhancement of ThT than that of intramolecular parallel and intermolecular antiparallel G4s. These DNA sequences were separated on native gels and stained by ThT for G4 and then by Stains-all (dye) for all DNA structures. Most of the sequences adopted parallel G4 multimers and intramolecular G4s in the presence of K+, meanwhile only a part of them formed G4 multimers and intramolecular structures in the presence of Na+. The optical density (OD) ratio of DNA bands stained by ThT and Stains-all were derived by ImageJ, and the ratios of G4 multimers were higher than 1.0, intramolecular parallel G4s were about 0.5, and non-G4s were near 0. Furthermore, the flanking nucleotides were favorable to the formation of multimers of c-Myc in K+ solutions, especially those flanking with T; while in Na+ solutions, only those sequences flanking with two or more A preferred to form G4 multimers. Our results suggest that the current strategy holds the potential for polymorphic study of G4s.

BoaγPLI: Structural and functional characterization of the gamma phospholipase A2plasma inhibitor from the non-venomous Brazilian snakeBoa constrictor.

Plasma in several organisms has components that promote resistance to envenomation by inhibiting specific proteins from snake venoms, such as phospholipases A2 (PLA2s). The major hypothesis for inhibitor’s presence would be the protection against self-envenomation in venomous snakes, but the occurrence of inhibitors in non-venomous snakes and other animals has opened new perspectives for this molecule. Thus, this study showed for the first time the structural and functional characterization of the PLA2 inhibitor from the Boa constrictor serum (BoaγPLI), a non-venomous snake that dwells extensively the Brazilian territory. Therefore, the inhibitor was isolated from B. constrictor serum, with 0.63% of recovery. SDS-PAGE showed a band at ~25 kDa under reducing conditions and ~20 kDa under non-reducing conditions. Chromatographic analyses showed the presence of oligomers formed by BoaγPLI. Primary structure of BoaγPLI suggested an estimated molecular mass of 22 kDa. When BoaγPLI was incubated with Asp-49 and Lys-49 PLA2 there was no severe change in its dichroism spectrum, suggesting a non-covalent interaction. The enzymatic assay showed a dose-dependent inhibition, up to 48.2%, when BoaγPLI was incubated with Asp-49 PLA2, since Lys-49 PLA2 has a lack of enzymatic activity. The edematogenic and myotoxic effects of PLA2s were also inhibited by BoaγPLI. In summary, the present work provides new insights into inhibitors from non-venomous snakes, which possess PLIs in their plasma, although the contact with venom is unlikely.

Improving emulsion stability based on ovalbumin-carboxymethyl cellulose complexes with thermal treatment near ovalbumin isoelectric point

Ovalbumin (OVA) is an important protein emulsifier. However, it is unstable near the isoelectric point pH, which limits its applications in the food industry. Polysaccharides may be explored to tackle this challenge by improving its pH-dependent instability. In this work, carboxymethyl cellulose (CMC) was used as a model polysaccharide to mix with OVA near its isoelectric point (pH 4.7) with subsequent mild heating at 60 °C for 30 min. The molecular interactions between OVA and CMC were comprehensively studied via a series of characterizations, including turbidity, zeta potential, intrinsic fluorescence, surface hydrophobicity, circular dichroism (CD) spectra and Fourier transform infrared spectroscopy (FTIR). The droplet sizes of the emulsions prepared by OVA-CMC were measured to analyze emulsifying property and stability. The results indicated that free OVA was easily aggregated due to loss of surface charges, while complexing with CMC significantly inhibited OVA aggregation before and after heating owing to the strong electrostatic repulsion. In addition, OVA exposed more hydrophobic clusters after heating, which resulted in the growth of surface hydrophobicity. Altogether, the heated OVA-CMC complexes presented the best emulsifying property and stability. Our study demonstrated that complexing OVA with CMC not only greatly improved its physicochemical properties but also significantly enhanced its functionality as a food-grade emulsifying agent, expanding its applications in the food industry, as development of emulsion-based acidic food products.

A new coumarin derivative from the stems of the endangered plant Ulmus elongata

A preliminary phytochemical investigation of the stems of the endangered plant Ulmus elongata led to the isolation of a new coumarin derivative (named ulmuselactone A, 1) and eight known compounds (2-9). The new structure was elucidated by detailed analysis of comprehensive spectroscopic methods, and its absolute configuration was established by comparing experimental and calculated electronic circular dichroism (ECD) spectra. The isolated compounds were evaluated for their antibacterial activities.

Interaction of tebuconazole with bovine serum albumin: determination of the binding mechanism and binding site by spectroscopic methods

This study investigates the interaction between tebuconazole and bovine serum albumin (BSA) in a physiological buffer (pH = 7.4) using the fluorescence quenching method to obtain the apparent binding constants (K) and number of binding sites (n) in the interaction between tebuconazole and BSA. The results revealed that tebuconazole can quench the intrinsic fluorescence of BSA through a static quenching procedure. It also shows that the thermodynamic parameters of enthalpy change (ΔH) and entropy change (ΔS) are negative, indicating that the interaction of tebuconazole with BSA is mainly driven by van der Waals forces and hydrogen bonds. The process of binding was a spontaneous process in which Gibbs free energy change was negative. The distance of r between the donor (BSA) and acceptor (tebuconazole) was calculated to be 0.68 nm based on Forster’s non-radiative energy transfer theory. Analysis of synchronous fluorescence, three-dimensional fluorescence and circular dichroism (CD) spectra demonstrates that tebuconazole can induce conformational changes of BSA.

A New Neolignan from Justicia Procumbens

A new neolignan, named (7′S,8′R)-5,3′-dimethoxy-4,4′,9′-trihydroxy-2-8′,9-O-7′-neolignan (1), along with two known compounds, secoisolariciresinol (2) and lariciresinol (3), was isolated from the whole plant of Justicia procumbens L. The structure of 1 was established by spectroscopic methods, and the absolute configuration was determined using circular dichroic (CD) spectra.

Synthesis and electronic properties of meso-tetra(3,4,5-trimethoxy)phenyl-porphyrin and -tetrabenzoporphyrin and their phosphorus complexes

meso-Tetra(3,4,5-trimethoxy)phenyl-porphyrin and -tetrabenzoporphyrin and their phosphorus complexes were synthesized and their electronic absorption and magnetic circular dichroism (MCD) spectra discussed based on TD-DFT molecular orbital (MO) calculations. Nucleus-independent chemical shift (NICS) and anisotropy of the induced current density (ACID) calculations were also carried out for metal-free (and phosphorus) tetrabenzoporphyrins in order to discuss the aromaticity and flow of electrons in the molecule.

Interaction Between α-Glucosidase Inhibitor with Common Blood Proteins: A Thermodynamic and Spectroscopic Studies

The interaction of an α-glucosidase inhibitors class of drug acarbose with globular proteins like bovine serum albumin (BSA), human serum albumin (HSA) and haemoglobin studied by fluorescence, circular dichroism (CD) spectroscopic methods. Acarbose is used for the treatment of diabetes mellitus type 2 and in some countries, prediabetes. The quenching constant (kq) values were calculated by using fluorescence data, higher with haemoglobin (at λext = 405 nm). It indicates the quenching process for the acarbose-haemoglobin interaction. Thus, the binding constants (kb), infers that the electrostatic, hydrogen bonding, and intermolecular interactions play an important role in the proteins, and drug interaction. The number of binding sites (n), between BSA, HSA and haemoglobin with acarbose was estimated by fluorescence data, the highest binding sites (15.55) of acarbose-haemoglobin at (λext = 405nm) indicates that the strong interaction or high quenching interaction. The interactions between BSA, HSA and haemoglobin with acarbose were confirmed by spectroscopic analysis and thermodynamic determination. The circular dichroism (CD) spectra implied the significant change in the conformation of BSA, HSA and haemoglobin upon binding with acarbose.

Anisotropic energy transfer in a clay-porphyrin layered system with environment-responsiveness.

The adsorption orientation behavior of tetrakis(1-methylpyridinium-3-yl)porphyrin (m-TMPyP) and tetrakis(1-methylpyridinium-4-yl)porphyrin (p-TMPyP) on the clay monolayer prepared by the Langmuir Blodgett (LB) technique was investigated using the absorption and dichroic spectra obtained on a waveguide. It was revealed that the orientation of m-TMPyP and p-TMPyP on the clay monolayer, that is parallel and tilted with respect to the clay surface, depends on the surrounding environments such as water and N,N-dimethylformamide (DMF). The anisotropic photochemical energy transfer between m-TMPyP as a donor and p-TMPyP as an acceptor in the layered system was investigated in water and in DMF-water (9/1 (v/v)) by a fluorescence observation. As a result, while energy transfer efficiency (ηET) was 60% for the parallel-parallel orientation in water, that was 10% for the tilted-tilted orientation in DMF-water (9/1 (v/v)). The major factor for the change of ηET could be a change of the distance between m-TMPyP and p-TMPyP, and the J value that is a parameter for spectral overlap between energy donor's fluorescence and acceptor's absorption.

Synthesis and biological activity study of the retro-isomer of RhTx against TRPV1.

TRPV1 is a ligand-gated ion channel and plays an important role in detecting noxious heat and pain with an unknown mechanism. RhTx from Chinese red-headed centipede activates the TRPV1 channel through the heat activation pathway by binding to the outer pore region, and causes extreme pain. Here, we synthesized RhTx and its retro-isomer RL-RhTx. Their structures were investigated by their circular dichroic spectra and NMR spectra. The effect of RhTx and RL-RhTx on the currents of wild-type and mutants of TRPV1 indicated that RL-RhTx have comparable TRPV1 activation responses to RhTx. A mutagenesis study showed that four TRPV1 residues, including Leu461, Asp602, Tyr632 and Thr634, significantly contributed to the activation effects of RL-RhTx and RhTx, and both peptides probably bind with TRPV1 in similar binding modes. As a novel TRPV1 activator, RL-RhTx provides an essential powerful tool for the investigation of activation mechanisms of TRPV1.

Effective structural chirality of beetle cuticle determined from transmission Mueller matrices using the Tellegen constitutive relations

Several beetle species in the Scarabaeoidea superfamily reflect left-handed polarized light due to a circular Bragg structure in their cuticle. The right-handed polarized light is transmitted. The objective here is to evaluate cuticle chiral properties in an effective medium approach using transmission Mueller matrices assuming the cuticle to be a bianisotropic continuum. Both differential decomposition and nonlinear regression were used in the spectral range of 500–1690 nm. The former method provides the sample cumulated birefringence and dichroic optical properties and is model-free but requires a homogeneous sample. The materials chirality is deduced from the circular birefringence and circular dichroic spectra obtained. The regression method requires dispersion models for the optical functions but can also be used in more complex structures including multilayered and graded media. It delivers the material properties in terms of model functions of materials’ permittivity and chirality. The two methods show excellent agreement for the complex-valued chirality spectrum of the cuticle.

Combination mode of antimalarial drug mefloquine and human serum albumin: Insights from spectroscopic and docking approaches.

The interaction between mefloquine (MEF), the antimalarial drug, and human serum albumin (HSA), the main carrier protein in blood circulation, was explored using fluorescence, absorption, and circular dichroism spectroscopic techniques. Quenching of HSA fluorescence with MEF was characterized as static quenching and thus confirmed the complex formation between MEF and HSA. Association constant values for MEF-HSA interaction were found to fall within the range of 3.79-5.73 × 104 M-1 at various temperatures (288, 298, and 308 K), which revealed moderate binding affinity. Hydrogen bonds and hydrophobic interactions were predicted to connect MEF and HSA together in the MEF-HSA complex, as deduced from the thermodynamic data (ΔS = +133.52 J mol-1 K-1 and ΔH = +13.09 kJ mol-1 ) of the binding reaction and molecular docking analysis. Three-dimensional fluorescence spectral analysis pointed out alterations in the microenvironment around aromatic amino acid (tryptophan and tyrosine) residues of HSA consequent to the addition of MEF. Circular dichroic spectra of HSA in the wavelength ranges of 200-250 and 250-300 nm hinted smaller changes in the protein's secondary and tertiary structures, respectively, induced by MEF binding. Noncovalent conjugation of MEF to HSA bettered protein thermostability. Site marker competitive drug displacement results suggested HSA Sudlow's site I as the MEF binding site, which was also supported by molecular docking analysis.

Bioactive terpenoids from Croton laui

Two new highly-oxygenated neo-clerodane diterpenoids, 3S-acetoxyl-mollotucin D dilactone ester (1) and 6S-crotoeurin C (2), and a new lupane-type triterpene, 16β-hydroxyl-3β-O-trans-coumaroyl-betulin (6), as well as three known analogues (3–5) were obtained from the leaves of Croton laui. The structures of the new compounds were determined by extensive spectroscopic methods, and their absolute configurations were determined by combination of single-crystal X-ray diffraction analysis, electronic circular dichroism (ECD) spectra, and literature data. Compounds 2 and 3 exhibited inhibitory activities of lipopolysaccharide (LPS)-induced nitric oxide (NO) production in RAW 264.7 macrophages with IC50 values of 1.2 and 1.6 μM, respectively. Additionally, compound 6 exhibited activity against Col205 and HepG2 cell lines with IC50 values of 12.9 and 17.7 μM, respectively.